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...43 66 62 68 90 63 89 65 85 58 49 81 49 76 73 48 77 NM_001001152 79 129 52 50 24 45 130 154 112 147 56 85 67 33 52 31 93 77 65 109 ... ... ... It has about 29000 rows and 20 columns (incl col.name). How would you set this up in edgeR if you want to compare the 10 first with the 10 last? -- View this message in context: http://r.789695.n4.nabble.com/edgeR-design-matrix-setup-tp4631094.html Sent from the R help mailing list archive at Nabble.com.

I know others have asked similar questions to the R developers, but I could not find the solution to this question. Please forgive me if I have missed a crucial point in a previous post. I would like to submit a package to CRAN that depends on the bioconductor package "edgeR". Listing "edgeR" under the Depends or Imports lines in the DESCRIPTION file for my package causes an error when running the `R CMD check' command on my package's 'tar.gz' file: * checking package dependencies ... ERROR Package required but not available: ?edgeR? I...

Hi, R-help, I have a group of data from RNA-seq want to be analyzed by Fisher's exact test in R. I want to compare the significant difference of about 30,0000 individuals in two different samples, and I have no idea how to use R, so could you please give me some suggestions or the scripts for Fisher's exact test? Thank you very much. Best, Guanfeng Wang [[alternative HTML version

I am running and analysis of sequencing data uisng the EdgeR package. I have received the following error: Using grid search to estimate tagwise dispersion. Error: cannot allocate vector of size 307.3 Mb indicating the memory allocation is too small. How would I change this confiuration in R so that the script can run with the files I have? Help appreciat...

Hello; Does anybody knows that R have a function for Generelized Negative Binomial model, something like "gnbreg" in "STATA" where dispersion parameter itself is a function of covaraites ? Thanks; [[alternative HTML version deleted]]

...tor Setup VGA+DVI - Geforce 8200 (Onboard; Jetway JNC62K) nouveau [ DEVICE][0000:02:00.0] Chipset: MCP77/MCP78 (NVAA) nouveau [ DEVICE][0000:02:00.0] Family : NV50 Versions: Kernel: 3.12.0 (vanilla), 3.8.0- (Mint Kernel) libdrm-nouveau2: 2.4.46+git20130910.58d00888-0ubuntu0sarvatt~raring (xorg-edgers ppa) xorg-server: 1.13.4~git20130508+server-1.13-branch.10c42f57-0ubuntu0ricotz~raring (xorg-edgers ppa) xserver-xorg-video-nouveau : : 1.0.9+git20130730.300c5a32-0ubuntu0sarvatt~raring (xorg-edgers ppa) vlc: 2.2.0~~git20131104+r3123-0~r114+113~ubuntu13.04.1 (ppa) -- You are receiving this mail...

Hello folks, just rebuilt the latest snapshot of OpenSSH from Damien's page using the latest beta of OpenSSL-0.9.6-beta3 and have good news: SSH2 works again! Any fellow bleeding-edgers want to confirm this? Btw, I tested this on i686/Linux. dtc --- Daniel T. Chen | chenda at cs.unc.edu

hello everyone. I have some troubles running games with wine. When i try to p:ay i cant see the models of any character, this happen in every game except for "cold fear". Somebody can help me to solve this problem? My OS is: Ubuntu 10.10-Maverick Meerkat My system spec are: Video: Ati radeon hd 5570 Ram: 2GB Motherboard: Amd Black Series A785GM-AD3 CPU: Amd Athlon II x3 435 Processor

When I could not plot by SciLab I installed Xorg-Edgers video. And WineHQ worked normally. WineHQ can't start after I installed the library libgl1-mesa-glx ( a workaround of the bug https://bugs.launchpad.net/ubuntu/+source/scilab/+bug/876195 ) and reverted to official Xorg by the command "sudo ppa-purge xorg-edgers": user at Notebook:~$...

I've tried to use Nouveau several times, with several operative systems (Ubuntu, Mint, Trisquel). Seemingly, the versions of Nouveau are too old, since my screen is detected as being smaller than it is. All in all, I tried to follow the instructions to build from scratch (in order to have the really latest version), and failed. Would somebody mind to create a script to download the sources,

I cant make the nouveau work with an arcade monitor, problably because the EDID. I can make modeline work fine to reduce the horizontal to 15khz, tested in a normal pc monitor (with ugly visual because the 15khz in horizontal). But when i try in the arcade monitor, dont show any image after xorg start. In official nvidia driver has an option NOEDID to force the driver to ignore information from

Dear all, I'm writing to ask for advice as to best practice. A PhD student working with me is writing C++ code that we hope to make public as src code in our Bioconductor package edgeR. He wants to call the function fmm_spline, which is part of the source code for the stats package http://svn.r-project.org/R/trunk/src/library/stats/src/splines.c, from his C++ code. This function isn't one of the entry points for C code documented in Chapter 6 of the "Writing R exte...

...ed in text files with the headers LANE, RNA_NAME, SEQ, and SEQCNT. I've been using x = "filename.txt" y = aggregate(x$SEQCNT, list(x$RNA_NAME), sum) write.table(y, "C:/path/filename.txt", sep="\t") to generate an output that I've analyzed using readDGE in the edgeR package: >RNA Targets = read.delim("Targets.txt", stringsAsFactors = FALSE) >Targets Files Groups A.txt 1 B.txt 2 >v = readDGE(Targets, skip = 5, comment.char = "!") I've done this several times; until yesterday, it worked fine. Today, however, an err...

...ng issues with Nouveau in Ubuntu 10.4. I posted on the forums, but the only help I have gotten had been people telling me to install the Blob (which is a P.O.S. in my opinion), so I have decided to ask the experts. Prior to my HDD failing, I was running Ubuntu 9.10 with Nouveau installed from the Edgers PPA without any issues. When I replaced the HDD, I went ahead and did a clean install of 10.4 and was delighted to find Nouveau as the default driver... yay! The only problem is that I seem to have an issue with dual heads. I have a pretty new computer (as of January) with a 1GB Nvidia card tha...

Hallo all, i didn't found any deb packages for ptalarbvorm so i did it by my self. currently i do it in my playgrond here https://launchpad.net/~bug-track/+archive/ppa probably it will be better to add ffmpeg2theora too. I stated write scrip to do it regularity without big work overhead. any comments? Regards, Alexey

...don't run. I can get installation screens, loading screens etc. but nothing past that. Have followed all instructions from AppDB and have everything set up the same as on my laptop where the games work. I have a feeling it has something to do with the nvidia proprietary drivers (using the xorg-edgers PPA). Here's what I'm getting: Code: Unhandled exception: page fault on read access to 0x00000000 in 32-bit code (0x0097690d). Register dump: CS:0073 SS:007b DS:007b ES:007b FS:0033 GS:003b EIP:0097690d ESP:0033f36c EBP:00b91bc0 EFLAGS:00210287( R- -- I S - -P-C) EAX:00000000 EBX:00...

Thanks for all your great answers. The app I?m working on is indeed an exploratory data analysis tool for gene expression, which requires a bunch of bioconductor packages. I guess for now, my best solution is to divide my app into modules and load/unload packages as the user switch from one module to another. This brought me another question: it seems that unload package with the

https://bugs.freedesktop.org/show_bug.cgi?id=68037 Priority: medium Bug ID: 68037 Assignee: nouveau at lists.freedesktop.org Summary: TRAP_TPDMA - TP0: Unhandled ustatus 0x00000008 ; and other NV50 log spam errors QA Contact: xorg-team at lists.x.org Severity: normal Classification: Unclassified

...AssignedTo: nouveau at lists.freedesktop.org ReportedBy: dirkneukirchen at web.de QAContact: xorg-team at lists.x.org Created attachment 53001 --> https://bugs.freedesktop.org/attachment.cgi?id=53001 dmesg with nonrelated errors removed System: - Ubuntu Oneiric with xorg-edgers ( - piglit from git Steps to reproduce: 1. running piglit env PIGLIT_BUILD_DIR=Programming/piglit ./piglit-run.py tests/sanity.tests results/sanity.results 2. readPixSanity tests create dmesg [ 7963.282652] [drm] nouveau 0000:02:00.0: PGRAPH - TRAP_TPDMA - TP0: Unhandled ustatus 0x00020000 [ 79...

...s. Lines can be drawn, but are NOT straight! Are there tools to change the size/position of highlights? Or to add highlights and underline words? Changing position/size manually by editing the data in the pdf-document is possible. Changing the color is more trickier (somehow possible in Microsoft Edger; though the direct approach to rewrite the actual stream is better). Maybe there are some tools to do it? Some R code is below. Sincerely, Leonard ######### library(zip) con = file("_some_pdf_.pdf", "rb") NL = 0 # - very dirty hack; # - assumes Annotations are in the last...